To date the majority of expression analysis has focused on the total amount of transcript. However, emerging evidence underlies the importance of understanding the allele specific transcript in cases of human disease. Human diseases are complex traits and understanding the nature of genetic variation underlying such complexity is one of the great challenges before the scientific community. Incorporating a basic understanding of the allele-specific nature of expression will allows us to address fundamental questions about quantitative inheritance in novel ways. Understanding quantitative inheritance at for allele specific transcription will help us understand and effectively model complex human disease. Since little is known about the mechanisms underlying allele specific expression, we need to begin with basic questions about the conditions under which allelic expression varies. What is the quantitative nature of such allele specific expression? Is it additive? Or is there evidence for dominance variation? Is allele specific expression caused by cis effects? trans effects? or the interaction between cis and trans effects? Drosophila is a model organism perfectly suited to understanding these basic questions. Full genome sequences for five divergent lines of D. simulans are readily available, chromosomal content can be manipulated in order to test experimentally the impact of specific alleles on transcription. In this proposal we seek to understand the basis for allele specific expression. We will accomplish this goal by i) developing a high density microarray platform that will allow us to assay allele specific expression in D. simulans ii) developing analytic tools that facilitate modeling of allele specific expression iii) examining the impact of maternal effects, dose response, additivity, and dominance on allele specific expression in a reciprocal reference mating design iv)Partitioning cis and trans variation from the interactions by developing a set of X chromosome substitution lines, and 3rd chromosome introgression lines and combining these into X substitution/ 3rd chromosome introgression lines. The immediate objective of this work is to understand how specific alleles are expressed, how that expression is influenced by cis and trans effects, and how classic quantitative genetics concepts of additivity and dominance are related to cis and trans effects. The long term objective is to understand how genetic variation contributes to complex, quantitative phenotypes such as human disease. [unreadable] [unreadable] [unreadable]